Unfortunately the built-in 'delete guides' menu item removes all guides [lines and points] in the model - including any in groups or component-instances [including locked ones] and even guides stored in 'off' layers - however, guides within a component definition that has no instances in the model are safe...
Two years ago I wrote a set of context-menu tools to deleted guide-lines / -points 'selectively' - here's an update ConsDeleteContext.rb I would also be possible to write a new tool to 'preserve selected guides' - it would duplicate them in a new definition that had no instances [with a bit of vertical 'edge' ([0,0,0],[0,0,1]) at the origin***], later you could choose to 'restored preserved guides' and it would place an instance of that component [at the origin, erasing the temporary 'edge' there ? *** I haven't quite worked through how the guide-component 'insertion' point is kept for later reinsertion - but it will be possible], then explode the instance and then delete that component-definition's entities, thereby purging it from the component-browser's list. Of course purging the model's unused components in between times would delete the preserved-guide component and the saved guides would be lost - just like copying something new to the clipboard loses the current data. The 'preserve selected guides' would be like using the clipboard and it'd overwrite any already preserved, but it could be set to warn if there is an existing preserved set [i.e not yet restored] that'd be lost in the process, and it'd ask you either to overwrite the set or to add these new guides to the existing set ?
Unfortunately I'm stowed under will other things, and I'm unlikely to be able to look at this before sometime in June! - but if anyone wants to take up the ideas feel free...